title: SE_skin4

value: Staphyloccocus epidermidis


title: SE_skin2

status: Public on Nov 11 2019

type: SRA

city: San Francisco

first: Tiffany

middle: C

last: Scharschmidt

state: CA

address: 513 Parnassus Ave, 1201B

department: Dermatology

country: USA

institute: University of California, San Francisco

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence and were aligned to UCSC GRCm38/mm10 reference genome with STAR software (2.4.2a)
SAM files were generated with SAMtools from alignment results
Read counts were obtained with htseq-count (0.6.1p1) with the union option
Differential expression was determined using the R/Bioconducter package DESeq2
Genome_build: Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: 060617_JLmerged_counts_SESAonly.csv: raw counts of sequencing reads
Supplementary_files_format_and_content: Results_SESAskin.csv: differential expression results from DESeq2

molecule: total RNA

organism: Mus musculus

source_name: Whole skin

growth_protocol: Specific-pathogen-free newborn C57BL6 mice were colonized with either  Staphylococcus epidermidis Tü3298 or Staphylococcus aureus SF8300 starting on day 3 of life and every other day thereafter until post-natal day 19 by pipetting 100 μl of bacterial suspension onto their skin and distributing evenly using a sterile PBS-soaked cotton-tipped swab.

extract_protocol:
Whole skin RNA was isolated using an adapted protocol of the Qiagen RNeasy Fibrous tissue kit. In brief, tissue pieces were removed from RNA later and placed immediately in the suggested digestion buffer before dissociation using Miltenyi M tube. The kit protocol with column RNA isolation and DNAse cleanup was subseuqently followed. RNA quality was checked by Agilent Bioanalyzer Chip.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were sacrificed at 21 days of age and the entire trunk skin harvested and lightly defatted. An 8mm punch biopsy was taken from the back skin and placed in RNA later, kept overnight at 4C and then stored in -80 until subsequent RNA extraction.

tag: tissue

value: Whole skin

tag: strain

tag: age

value: post natal day 21

tag: tissue source

value: skin

tag: bacteria


title: SE_skin1


title: SUDHL1_DMSO_24h_1

city: Memphis

first: Chao-Yie

last: Yang

state: Tennessee

address: 881 Madison Avenue, Rm559

department: Pharmaceutical Sciences

institute: University of Tennessee HSC

description:
DMSO_24h_116838
processed data file: LBAI_WANG_SUDHL1_STAT3_2019.csv

data_processing:
RTA version 1.18.66.3 (HCS version 2.2.68 ) was used for basecalling.
bcl2fastq version 2.17.1.14 was used for generation fastq files.
Read alignment was done using Bowtie v0.12.8, with parameters “-k 100”.
Gene abundance estimation was done using rSeq v0.2.2, with parameters “-expression_analysis”.
Transcriptome annotation: GENCODE v24 basic.
Genome_build: NCBI GRCh38.p5
Supplementary_files_format_and_content: RPKM values of each cell line treated with DMSO, SD36, SD36Me.

organism: Homo sapiens

source_name: SU-DHL-1 cells

growth_protocol: Cells were grown in RPMI 1640 medium containing 10% fetal bovine serum, 50 units/mL penicillin and 100 µg/mL streptomycin and incubated at 37°C with 5% CO2.

extract_protocol:
Cells were collected at the end of treatment and total RNA was purified using RNeasy Mini Kit from Qiagen. RNA was assessed for quality using the TapeStation (Agilent). Samples with RINs (RNA Integrity Numbers) of 8 or greater were ribosomal RNA depleted using Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Illumina).
RNA libraries were prepared from the rRNA-depleted total RNA using TruSeq RNA Library Prep v2 kit (Illumina) following Illumina's standard protocol. Where the entire fraction of 0.1-3ug of rRNA depleted total RNA was fragmented and copied into first strand cDNA using reverse transcriptase and random primers. The 3 prime ends of the cDNA were then adenylated and adapters were ligated. One of the adapters that was ligated had a 6 nucleotide barcode that was unique for each sample which allowed us to sequence more than one sample in each lane of a HiSeq flow cell (Illumina). The products are purified and enriched by PCR to create the final cDNA library. Final libraries were checked for quality and quantity by TapeStation (Agilent) and qPCR using Kapa’s library quantification kit (Kapa Biosystems) for Illumina Sequencing platforms.

treatment_protocol: Cells were treated with DMSO (0.05% v/v), SD36 (1000 nmol/L) or SD36Me (1000 nmol/L) for 8 or 24 hours before collected for RNA isolation.

tag: cell line

tag: cell source

value: Lymph node

tag: genetic background

value: 88 chromosomes; t(2;5)(p23;q35) translocation

tag: molecular subtype

value: anaplastic large cell lymphoma

tag: treatment

value: DMSO

tag: treatment duration


title: SA_Treg5

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence and were aligned to UCSC GRCm38/mm10 reference genome with STAR software (2.4.2a)
SAM files were generated with SAMtools from alignment results
Read counts were obtained with htseq-count (0.6.1p1) with the union option
Differential expression was determined using the R/Bioconducter package DESeq2
Genome_build: Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Merged_counts_SESA_Treg_2017-3-9.csv: raw counts of sequencing reads
Supplementary_files_format_and_content: 2019-4-9_SESA_Treg_Results.csv: differential expression results from DESeq2

source_name: Skin regulatory T cells

extract_protocol:
RNA isolation was performed by Expression Analysis Q2 Solutions using QIAGEN RNeasy Spin columns and was quantified via Nanodrop ND-8000 spectrophotometer. RNA quality was checked by Agilent Bioanalyzer Chip.
The SMARTer Ultra Low input kit was used to generate cDNA libraries

treatment_protocol: To isolate skin T cells for staining and FACS sorting, mice were sacrificed at 21 days of age and the entire trunk skin harvested and lightly defatted. Skin was then minced with scissors and re-suspended in a 50ml conical with 1-2 ml of digestion media comprised of 2mg/ml collagenase XI, 0.5mg/ml hyaluronidase and 0.1 mg/ml DNase in RPMI with 1% HEPES, 1% penicillin-streptomycin and 10% fetal calf serum. This mixture was incubated in a shaking incubated at 37°C at 250 rpm for 45 min. An additional 15 ml of RPMI/HEPES/P-S/FCS media was then added and the 50 ml conical was shaken vigorously by hand for 30 s. Another 15 ml of media was added and then the entire suspension was filtered through a sterile 100 mm cell strainer followed by a 40 mm cell strainer into a new 50 ml conical. The suspension was then pelleted and the cell pellet was re-suspended in sort buffer (RPMI, 2 mM EDTA, 25mM HEPES, 2% FBS) with U/ml RiboLock RNase inhibitor (Thermo Scientific) for staining for 30 min at 4°C with fluorophore-conjugated antibodies specific for CD3, CD4, CD8, CD25, CD45, ICOS, TCRβ, and Tonbo Live-dead Ghost Dye. CD4 Teff (Live, CD45+, CD3int, CD4+, CD8neg, TCRβ+ CD25neg, ICOSneg) cells and Tregs (Live, CD45+, CD3int, CD4+, CD8neg, TCRβ+ CD25hi, ICOShi) were then isolated via cell sorting on a MoFlo XDP (Beckman Coulter) in the UCSF Flow Cytometry Core. Cells were pelleted and flash frozen.

tag: cell type

value: Skin regulatory T cells

value: Staphyloccocus aureus


title: SUDHL1_DMSO_24h_2

description:
DMSO_24h_116839
processed data file: LBAI_WANG_SUDHL1_STAT3_2019.csv


title: WT_rep2: Wild type strains replicate 2

type: mixed

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

hyb_protocol: A mixture of RNA from WT or mutant strains and gDNA pool was diluted in 50 µl Agilent hybridization buffer, and hybridized at a temperature of 60°C for 17 hours in a dedicated hybridization oven

scan_protocol: 100% PMT using Agilent scanner

data_processing: Local background-subtracted signals were corrected for unequal dye incorporation or unequal load of labelled product. The algorithm consisted of a rank consistency filter and a curve fit using the default LOWESS (locally weighted linear regression) method

label: cyanine 3

organism: Staphylococcus aureus subsp. aureus str. Newman

source_name: Newman WT

label_protocol: Incorporation of cyanine dye during reverse transcription

growth_protocol: S. aureus strains were grown in B medium

extract_protocol: Briefly, bacteria were lysed in 1 ml of Trizol reagent (Invitrogen Life Technologies, Karlsruhe, Germany) with 0.5 ml zirconia-silica beads (0.1 mm-diameter) in a high-speed homogenizer (Savant Instruments, Farmingdale, NY). RNA was isolated as described in the instructions provided by the manufacturer of Trizol. RNA isolation after phagocytosis was performed as described in the instructions provided by the manufacturer of the RNA isolation kit (ExpressArt RNAready, AmpTec) with the modification adding an inhibitor removal buffer (high pure viral nucleic acid kit, Roche diagnostics) in the first step. Then DNA digestion was performed as instructed by the RNA isolation kit.

treatment_protocol: no treatments

value: S. aureus strains grown in B medium

tag: genotype/variation

value: WT

label: cyanine 5

molecule: genomic DNA

source_name: gDNA pool

value: Staphylococcus aureus gDNA mixture


title: SUDHL1_SD36_24h_1

description:
SD36_24h_116842
processed data file: LBAI_WANG_SUDHL1_STAT3_2019.csv


title: MOLM16_SD36_24h_1

description:
SD36_24h_108229
processed data file: LBAI_WANG_MOLM16_STAT3_2019.csv

source_name: MOLM-16 cells

value: Hematopoietic/Lymphoid tissue

value: adult acute myeloid leukemia


title: sub_INF001_109039

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description:
INF001
fertility.results.csv.gz, responder.results.csv.gz

library_source: genomic

data_processing:
Basic read quality was verified using summaries produced by FastQC. Trimmomatic was used to remove low quality reads and bases
The reads for each sample were mapped to the human (GRCh38) genome using Bowtie2
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 1000 bp windows. The edgeR Pvalue was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR P value less than an arbitrarily chosen threshold were considered DMR. The DMR edges were extended until no genomic window with an edgeR P value less than 0.1 remained within 1000 bp of the DMR.
The selected DMR were then summarized and annotated.
Genome_build: GRCh38
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window and other summary values.

source_name: Sperm

growth_protocol:
A single center (Urology Department at Hospital Universitari i Politècnic La Fe), prospective and open clinical study. The IRB approval code protocol 2015-002521-19. We included two groups (infertility vs fertility). The infertility men (inability of the couple to become pregnant after one year of sexual activity), included caucasians between 25-45 years of age with a total sperm concentration (concentration in millions/mL x volume in mL) between 1-10 million (oligozoospermia) in at least 2 spermiograms obtained after a 2-4 day period of sexual abstinence and with a 7-day separation period between tests. The hormone profile used inclusion criteria of FSH 2-12 IU/mL, total testosterone >300 ng/mL and bioavailable testosterone (calculated with the Sexual Hormone Binding Globulin or SHBG albumin) >145 ng/dL. The fertile control group included caucasians without vasectomy and had a child in the last five years with a sperm concentration and motility above the 50th percentile according
to the parameters set forth in the 5th edition of the World Health Organization (WHO) guidelines in at least two spermiograms obtained after a 2-4 day period of sexual abstinence and with a 7-day period between tests. The hormones profiled used inclusion criteria of estradiol <50 pg/mL, FSH <4.5 IU/L, total testosterone >300 ng/dL and bioavailable testosterone >145
ng/dL.

extract_protocol:
Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed as follows: individual sperm DNA samples were diluted to 130 μl with 1x Tris-EDTA (TE, 10 mM Tris, 1 mM EDTA) and sonicated with a the Covaris M220 using the 300 bp setting. Fragment size was verified on a 2% E-gel agarose gel. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube and the volume was measured. The sonicated DNA was then diluted with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) to 400 μl, heat-denatured for 10 min at 95 C, then immediately cooled on ice for 10 min. Then 100 μl of 5X IP buffer and 5 μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4 C. The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 mL 1XPBS with 0.1% BSA and 2mM EDTA) was added and the bead sample was resuspended. The tube was then placed into a magnetic rack for 1-2 minutes and the supernatant was discarded. The tube was removed from the magnetic rack and the beads were washed once. The washed beads were resuspended in the same volume of 1xIP buffer (50 mM sodium phosphate ph7.0, 700 mM NaCl, 0.25% TritonX-100) as the initial volume of beads. 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2h on a rotator at 4 C. After the incubation the bead-antibody-DNA complex was washed three times with 1X IP buffer as follows: The tube was placed into a magnetic rack for 1-2 minutes and the supernatant was discarded, then washed with 1xIP buffer 3 times. The washed bead-DNA solution was then resuspended in 250 μl digestion buffer with 3.5 μl Proteinase K (20mg/ml). The sample was then incubated for 2-3 hours on a rotator at 55 C and then 250 μl of buffered Phenol-Chloroform- Isoamylalcohol solution was added to the sample and the tube was vortexed for 30 sec and then centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250 μl chloroform were added to the supernatant from the previous step, vortexed for 30 sec and centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol were added and mixed well, then precipitated in -20 C freezer for 1 hour to overnight. The precipitate was centrifuged at 14,000rpm for 20min at 4˚C and the supernatant was removed, while not disturbing the pellet. The pellet was washed with 500μl cold 70% ethanol in -20 C freezer for 15 min. then centrifuged again at 14,000rpm for 5min at 4 C and the supernatant was discarded. The tube was spun again briefly to collect residual ethanol to the bottom of the tube and as much liquid as possible was removed with gel loading tip. The pellet was air-dried at RT until it looked dry (about 5 minutes) then resuspended in 20μl H2O or TE. DNA concentration was measured in Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212)
The MeDIP DNA samples were used to create libraries for next generation sequencing (NGS) using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each sample received a separate index primer.

treatment_protocol: The infertility group received 150 IU of urinary or recombinant FSH three times per week for 12 weeks and the fertile control group did not received treatment. After three months of treatment, semen analysis and hormone profiles were retested in both groups. A validation set of samples collected that were selection failures due to a variety of reasons and not used in the infertility DMR analysis for DMR identification.

tag: fertility

value: infertile

tag: treatment response

value: non-responder

tag: selection failure

value: no


title: MOLM16_SD36_8h_1

description:
SD36_8h_108227
processed data file: LBAI_WANG_MOLM16_STAT3_2019.csv


title: MOLM16_DMSO_8h_2

description:
DMSO_108220
processed data file: LBAI_WANG_MOLM16_STAT3_2019.csv


title: SA_Treg3


title: MOLM16_SD36_8h_2

description:
SD36_8h_108228
processed data file: LBAI_WANG_MOLM16_STAT3_2019.csv


title: SE_Treg5

value: Staphyloccocus epidermidis


title: SA_Treg2

value: post natal day 21


title: SE_skin5

value: Whole skin

value: skin


title: MOLM16_DMSO_8h_1

description:
DMSO_108219
processed data file: LBAI_WANG_MOLM16_STAT3_2019.csv


title: siRE day2 DNaseI

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

description: transfection with RUNX1-ETO siRNA

data_processing:
The raw sequence reads in fastq format returned by the Illumina Pipeline was aligned to the hg38 human genome build using Bowtie
The reads in the resulting alignment files were used to generate density maps using bed-tools (Quinlan and Hall, 2010)
Regions of enrichment (DHS) of  DNAse1 sequencing data were identified using MACS2 (Zhang et al., 2008)
Genome_build: hg38
Supplementary_files_format_and_content: wiggle

source_name: siRE DNaseI 2 days after RUNX1/ETO knockdownfrom Kasumi1 cells

extract_protocol:
DNaseI digestions were performed  by adding DNaseI in the presence of NP40 to intact cells and digesting for just 3 min (Bert et al., 2007). A range of DNase I concentrations were used to achieve the optimal digestion, with the amount varying depending on the cell type and the concentration of cells in the reaction. Briefly, permeabilized cells were digested in DNase I buffer (60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 100 mM Tris-HCl pH 7.4, 1 mM EGTA pH 7.4, 0.3 M sucrose, 0.2% NP40, 1 mM CaCl2 and DNase I) Digestions were carried out at 22oC for 3 minutes and SDS was then added to a final concentration of 0.5% to terminate the reaction. Cell lysates were treated with 0.5 mg/ml Proteinase K at 37oC overnight followed by 0.2 mg/ml RNase A at 37oC for 1 hour. DNA was purified by phenol/chloroform extraction. For DNase-Seq, samples were first analyzed by qPCR to identify the optimally digested samples. The ratio of PCR signal was determined between active regions which were expected to be DNase I hypersensitive and inactive regions which should not be cleaved. Optimally digested samples gave a ratio of 0.4 to 0.7 for active/inactive. DNA fragments (~80-250 bp) were isolated from favourable samples by agarose gel extraction and further validated by qPCR analysis before library preparation. Primer pairs used to validate samples were, for the active region: TBP promoter and for the inactive region, a gene desert on chr 18.
DNA libraries from the chromatin immunoprecipitation assays were prepared using the Kapa Hyper-Prep kit according the manufacturer’s guidelines. Libraries were indexed and then amplified by PCR. Libraries were gel purified to ensure the correct fragment lengths were sequenced (Qiagen Gel purification Kit). Fragments of 200-300bp were selected for DNase I libraries and 200-400bp for ChIP libraries. Libraries were validated by qPCR and quantified using the Kapa quantification kit before pooling and sequencing on NextSeq® 500/550 High Output kit v2 75 cycles (Illumina, FC 404-2005).
DNaseI-Seq

value: Kasumi-1 cells


title: SE_Treg4


title: SE_Treg3


title: SE_Treg2


title: siRE day10 DNaseI

description: transfection with RUNX1-ETO siRNA

source_name: siRE DNaseI 10 days after RUNX1/ETO knockdownfrom Kasumi1 cells


title: Control mismatch day10 DNaseI

description: transfection with scrambled siRNA

source_name: Control DNaseI from Kasumi1 cells


title: Control mismatch day2 DNaseI

description: transfection with scrambled siRNA


title: SE_skin3


title: MOLM16_SD36_24h_2

description:
SD36_24h_108230
processed data file: LBAI_WANG_MOLM16_STAT3_2019.csv


title: SA_Treg4


title: SE_Treg1


title: siRE CTCF ChIP

description: transfection with RUNX1-ETO shRNA

data_processing:
The raw sequence reads in fastq format returned by the Illumina Pipeline was aligned to the hg38 human genome build using Bowtie
The reads in the resulting alignment files were used to generate density maps using bed-tools (Quinlan and Hall, 2010)
Regions of enrichment (peaks) of ChIP and DNAse1 sequencing data were identified using MACS (Zhang et al., 2008) and Dfilter software. The resulting peaks common for the two peak calling methods were considered for further analysis
Genome_build: hg38
Supplementary_files_format_and_content: wiggle

source_name: siRE CTCF ChIP after RUNX1/ETO knockdownfrom Kasumi1 cells

extract_protocol:
Chromatin Immunoprecipitation was carried out as described previously. Cells were re-suspended at 3.3x106 cells/ml and crosslinked for 45 minutes with 0.83 mg/ml Di(N-succinimidyl) glutarate (DSG – sigma). Cells were washed four times with PBS before re-suspending at 2x106 cells/ml and crosslinking for 10 minutes with 1% formaldehyde (Pierce) in PBS. Reactions were quenched with 0.4 M glycine, washed twice with PBS and incubated with Buffer A (10 mM HEPES pH 8.0, 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X-100) at 4oC for 10 minutes followed by Buffer B (10 mM HEPES pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.01% Triton X-100, 0.25% SDS) at 4oC for 10 minutes. Chromatin was sheared (?cells/ml) in IP Buffer I (25 mM Tris 1 M, pH 8.0, 150 mM NaCl, 2 mM EDTA, pH 8.0, 1% TritonX-100 and 0.25 % SDS) using a PicorupterTM (Diagenode) to fragments of ~500bp. The supernatant was collected and diluted 3-fold in IP Buffer II (25 mM Tris, pH 8.0, 150 mM NaCl, 2 mM EDTA, pH 8.0, 1% TritonX-100, 7.5 % glycerol). Chromatin from 2x106 cells was incubated with 2 ug JunD (?), STAT5 (?) coupled to 15 l protein G Dynabeads (Dynal) for 2 hours at 4oC. Beads were washed with Buffer 1 (20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 2 mM EDTA, pH 8.0, 1 % TritonX-100, 0.1 % SDS), twice with Buffer 2 (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, pH 8.0, 1 % TritonX100, 0.1 % SDS), LiCl buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1 mM EDTA, pH 8.0, 0.5 % NP40, 0.5 % Na-deoxycholate) and twice with TE/NaCl buffer (10 mM Tris-HCl pH 8.0, 50 mM NaCl, 1 mM EDTA). Samples were eluted in 100 l elution buffer (100 mM NaHCO3, 1% SDS) and crosslinks were reversed overnight at 65oC with proteinase K. DNA was purified using Agencourt AMPure (Beckman Coulter) according to the manufacturer’s instructions. Samples were analysed and validated by qPCR.
DNA libraries from the chromatin immunoprecipitation assays were prepared using the Kapa Hyper-Prep kit according the manufacturer’s guidelines. Libraries were indexed and then amplified by PCR. Libraries were gel purified to ensure the correct fragment lengths were sequenced (Qiagen Gel purification Kit). Fragments of 200-300bp were selected for DNase I libraries and 200-400bp for ChIP libraries. Libraries were validated by qPCR and quantified using the Kapa quantification kit before pooling and sequencing on NextSeq® 500/550 High Output kit v2 75 cycles (Illumina, FC 404-2005).

treatment_protocol: Kasumi-1 cells were electroporated with 200nm siRNA, in 700 μl of culture medium at a density of 1 × 107/ml. The Fischer EPI 3500 electroporator (Fischer, Heidelberg,Germany) was used for all transfections with the parameters set as 350V for 10ms. Post transfection, cells were maintained as described in section 2.1. RUNX1-ETO knockdown was conducted with the following siRNAs: RUNX1-ETO siRNA (sense, 5′-CCUCGAAAUCGUACUGAGAAG-3′ antisense, 5′-UCUCAGUACGAUUUCGAGGUU-3), mismatch control siRNA (sense, 5′-CCUCGAAUUCGUUCUGAGAAG-3′ antisense, 5′-UCUCAGAACGAAUUCGAGGUU-3

tag: target

value: CTCF

tag: chip antibody


title: Control mismatch LDB1 ChIP

description: transfection with scrambled shRNA

source_name: Control LDB1 ChIP from Kasumi1 cells


title: SA_Treg1

tag: strain


title: WT Mock β-catenin ChIP-seq Rep1

city: Minneapolis

first: Ying

last: Zhang

state: MN

address: 117 Pleasant St S.E.

department: Minnesota Supercomputing Institute

institute: University of Minnesota

description:
WT_Mock-1_S26
ChIP DNA
processed data file: WT_Mock_peaks.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence quality was accessed via FastQC, and none of the preprocessing (trimming, filtering or masking) is necessary.
RNA-seq:
Raw paired-reads were mapped to mouse genome (GRCm38) using HiSat2 with default parameters.
Raw counts of reads uniquely mapped to each gene in the GRCm38 Ensembl annotation (Mus_musculus.GRCm38.83.gtf) were calculated using Subread.
ChIP-seq:
Raw single-end reads were mapped to mouse genome (GRCm38) using BWA with default mapping parameters except for "-t 8".
MACS2 was used to identify Wnt3a binding peaks in comparison to mock samples with following parameters: -f BAM -g mm -B --broad --broad-cutoff 0.1
IgG and Input ChIP samples were not used in final analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: subread.txt: Tab-delimited text file includes raw counts.
Supplementary_files_format_and_content: *_Mock_peaks.txt: MACS2 peak files.

source_name: mIMCD3 cells

growth_protocol: mIMCD3 WT and HNF-1β deficient cells were maintained in DMEM with 10% FBS until 80-90% confluent and changed with fresh medium for 16hrs, cells were fully confluent for total RNA harvesting and ChIP fixation.

extract_protocol: Genomic DNA were prepared by SimpleChIP Plus Enzymatic Chromatin IP Kit (Cell Signaling). ChIP-seq libraries were made by ThruPLEX DNA-seq Kit (Rubicon Genomics).

treatment_protocol: Cells were treated with Mock (DMEM medium) or Wnt3a (100ng/ml) for 16hrs in DMEM + 10% FBS.

value: Renal epithelial cell line

tag: passage

value: Mock

value: alpha-beta-catenin (Cell Signaling #8480S, Lot5)


title: WT Wnt3a β-catenin ChIP-seq Rep2

description:
WT_Wnt3a-2_S31
ChIP DNA
processed data file: WT_Mock_peaks.txt


title: WT Mock β-catenin ChIP-seq Rep2

description:
WT_Mock-2_S30
ChIP DNA
processed data file: WT_Mock_peaks.txt


title: WT Wnt3a β-catenin ChIP-seq Rep1

description:
WT_Wnt3a-1_S27
ChIP DNA
processed data file: WT_Mock_peaks.txt


title: Control mismatch CTCF ChIP

description: transfection with scrambled shRNA

source_name: Control CTCF ChIP from Kasumi1 cells


title: WT Input DNA

description:
WT_Input_S22
Input DNA


title: Dstp_rep1: stp mutant replicate 1

source_name: Newman Dstp

tag: tissue

value: S. aureus strains grown in B medium

value: Dstp


title: HNF-1β KO Wnt3a β-catenin ChIP-seq Rep1

description:
KO_Wnt3a-1_S29
HNF-1β -/-
ChIP DNA
processed data file: KO_Mock_peaks.txt

value: HNF-1beta -/-


title: 833K-B4_rep3

city: Urbana

last: Spinella

state: IL

address: 2001 S Lincoln Ave

department: Comparative Biosciences

institute: University of Illinois at Urbana-Champaign

description:
processed data file: 833K_GEO_Processed.txt
833K_B4_UT_3_TACCGAGG-CCTGAACT_L00M

data_processing:
fastq files were aligned to human genome assembly NCBI GRCh38.p12 using STAR aligner .
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was TMM normalized using the calcNormFactors function in R
Differentially expressed genes (³2-fold and £1% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma trend package.
Genome_build: human genome assembly NCBI GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files includeTMM normalized counts per million (CPM) values for each Sample ...

source_name: Derived from 833K

growth_protocol: All cells were cultured in DMEM with 10% FBS and antibiotic in incubator (5% CO2; 37°C)

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the HiSeq 4000 sequencing kit version 1, according to the manufacturer’s instructions.

value: Embryonic carcinoma

tag: tissue origin

value: testis

tag: cisplatin sensitivity

value: Cisplatin acquired resistant


title: 833K-A2_rep2

description:
processed data file: 833K_GEO_Processed.txt
833K_A2_UT_2_GTCGGAGC-GGTTATAA_L00M


title: 833K-B4_rep1

description:
processed data file: 833K_GEO_Processed.txt
833K_B4_UT_1_GGCATTCT-CTAGCTTG_L00M


title: HNF-1β KO Mock β-catenin ChIP-seq Rep2

description:
KO_Mock-2_S32
HNF-1β -/-
ChIP DNA
processed data file: KO_Mock_peaks.txt

tag: cell line


title: 833K-A2_rep3

description:
processed data file: 833K_GEO_Processed.txt
833K_A2_UT_3_CTTGGTAT-CCAAGTCC_L00M


title: 833K-A2_rep1

description:
processed data file: 833K_GEO_Processed.txt
833K_A2_UT_1_ACTAAGAT-AACCGCGG_L00M


title: 833K_rep3

description:
processed data file: 833K_GEO_Processed.txt
833K_UT_3_GGTACCTT-AAGACGTC_L00M

source_name: Testicular embryonal carcinoma cell lines derived from metastatic site; Abdomen


title: HNF-1β KO Mock IgG

description:
KO_IgG_S25
HNF-1β -/-
ChIP DNA

value: Normal IgG (Cell Signaling #2729S, Lot7)


title: HNF-1β KO Mock β-catenin ChIP-seq Rep1

description:
KO_Mock-1_S28
HNF-1β -/-
ChIP DNA
processed data file: KO_Mock_peaks.txt


title: HNF-1β KO Wnt3a β-catenin ChIP-seq Rep2

description:
KO_WNT3a-2_S33
HNF-1β -/-
ChIP DNA
processed data file: KO_Mock_peaks.txt


title: 833K_rep1

description:
processed data file: 833K_GEO_Processed.txt
833K_UT_1_ATGTAAGT-ACTCTATG_L00M


title: 2102EP-C1_rep3

description:
processed data file: EP_GEO_Processed.txt
2102EP_C1_UT_3_TGCGGCGT-CCTCGGTA_L00M

source_name: Derived from 2102EP


title: WT Wnt3a RNA-seq Rep2

description:
WT-Wnt3A_2
processed data file: subread.txt

extract_protocol: Total RNA was isolated using a RNeasy kit (QIAGEN). RNA samples passed the quality control (RIN>8) were used to create a polyA barcoded RNAseq libraries using standard Illumina TruSeq protocols.

value: WT


title: siRE LDB1 ChIP

description: transfection with RUNX1-ETO shRNA

source_name: siRE LDB1 ChIP after RUNX1/ETO knockdownfrom Kasumi1 cells


title: HNF-1β KO Input DNA

description:
KO_Input_S23
HNF-1β -/-
Input DNA


title: 2102EP-C1_rep2

description:
processed data file: EP_GEO_Processed.txt
2102EP_C1_UT_2_GAATGAGA-GAGGCATT_L00M


title: 2102EP-C1_rep1

description:
processed data file: EP_GEO_Processed.txt
2102EP_C1_UT_1_AGGCAGAG-AGAATGCC_L00M


title: WT Mock IgG

description:
WT_IgG_S24
ChIP DNA


title: WT Mock RNA-seq Rep2

description:
WT-Mock_2
processed data file: subread.txt


title: 833K-B4_rep2

description:
processed data file: 833K_GEO_Processed.txt
833K_B4_UT_2_AATGCCTC-TCGATCCA_L00M


title: 2102EP-B3_rep2

description:
processed data file: EP_GEO_Processed.txt
2102EP_B3_UT_2_GCGCTCTA-GCTCCGAC_L00M


title: 2102EP-B3_rep3

description:
processed data file: EP_GEO_Processed.txt
2102EP_B3_UT_3_AACAGGTT-ATACCAAG_L00M


title: WT Mock RNA-seq Rep1

description:
WT-Mock_1
processed data file: subread.txt


title: WT Wnt3a RNA-seq Rep1

description:
WT-Wnt3A_1
processed data file: subread.txt


title: WT Mock RNA-seq Rep3

description:
WT-Mock_3
processed data file: subread.txt


title: WT Wnt3a RNA-seq Rep3

description:
WT-Wnt3A_3
processed data file: subread.txt


title: 2102EP-B3_rep1

description:
processed data file: EP_GEO_Processed.txt
2102EP_B3_UT_1_ATATCTCG-ATCTTAGT_L00M


title: 833K_rep2

description:
processed data file: 833K_GEO_Processed.txt
833K_UT_2_GCACGGAC-GTCTCGCA_L00M


title: HNF-1β KO Wnt3a RNA-seq Rep2

description:
HNF1bKO-Wnt3A_2
HNF-1β -/-
processed data file: subread.txt


title: HNF-1β KO Wnt3a RNA-seq Rep1

description:
HNF1bKO-Wnt3A_1
HNF-1β -/-
processed data file: subread.txt


title: 2102EP-A1_rep1

description:
processed data file: EP_GEO_Processed.txt
2102EP_A1_UT_1_AAGATACT-ACTTACAT_L00M


title: HNF-1β KO Mock RNA-seq Rep2

description:
HNF1bKO-Mock_2
HNF-1β -/-
processed data file: subread.txt


title: 2102EP_rep3

description:
processed data file: EP_GEO_Processed.txt
2102EP_UT_3_TAAGTGGT-CTTAAGCC_L00M

source_name: Testicular embryonal carcinoma cell lines derived from retroperitoneal lymph node

value: Cisplatin sensitive


title: 2102EP-A1_rep2

description:
processed data file: EP_GEO_Processed.txt
2102EP_A1_UT_2_GGAGCGTC-GTCCGTGC_L00M


title: 2102EP_rep1

description:
processed data file: EP_GEO_Processed.txt
2102EP_UT_1_TCGTAGTG-AGACTTGG_L00M


title: cko

city: New Haven

first: Yajaira

last: Suarez

state: Connecticut

address: 10 Amistad Street

department: Comparative Medicine

institute: Yale University School of Medicine

description: 3 pooled biological replicates

data_processing:
The tagged libraries were sequenced on HiSeq2500.  The sequencing files were processed the cellranger.
The output of the cellranger was procssed with Seurat.
The data was visuatilized using R
Genome_build: mm10
Supplementary_files_format_and_content: The processed data has three files, the barcodes.csv, the genes.csv, and matrix.mtx.  Each sample generates 3 such files.  All of these files are required by Seurat to process the data.

source_name: CD45 cells pooled from LLC tumors of  3 mir-21flox/flox mice

growth_protocol: LLC cells were subqutaneously implated in WT or miR-21 null mice. After 14 days tumors were isolated digested and TAMs  were FACS sorted as (CD45+, CD11b+, MHCII+, F4/80+)

extract_protocol:
Sorted cells were counted and assessed for viability with Trypan Blue using a Countess II automated counter (Invitrogen), and adjusted at a concentration of 800-1000 cells/µL. Final cell viability estimates ranged between 80-93%. Single cell suspensions were loaded onto 10X Genomics Single Cell A Chips (10x Genomics, PN-120236) along with the reverse transcription (RT) master mix as per the manufacturer's protocol for the Chromium Single Cell 3' Reagent kits V2. (10X Genomics; PN-120237), to generate single cell gel beads in emulsion (GEMs) and sequencing libraries.
Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10xGenomics) using manufacturer protocol
The Single Cell 3’ Protocol produces Illumina-ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired-end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1, while Read 2 is used to sequence the cDNA fragment. Sample index sequences are incorporated as the i7 index read. Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired-end sequencing.
Rapid mode as follows: 26 bp (Read 1); 8bp (i7 Sample Index); 0bp (i5 Index); 98bp (Reads 2).The BCL data will include the paired-end Read 1 (containing the 16 bp 10x Barcode and 10 bp UMI) and Read 2 and the sample index in the i7 index read.

tag: age


title: miRKoX

description:
Biological Replicate 4
miRKOX_TAATGCGC

data_processing:
Alignment was done against the Genome Reference Consortium Mouse Build 38 (mm10) with the STAR aligner using Partek Flow software version 7.0, build 7.18.0130. Copyright ©; 2018 Partek Inc., St. Louis, MO, USA
Aligned reads were quantified by using the  mm10 - Ensembl Transcripts release 91 as annotation model
Raw read counts were normalized and 10E-04 was added to all the samplesusing Partek Flow
Genome_build: Genome Reference Consortium Mouse Build 38 (mm10)
Supplementary_files_format_and_content: tab-delimited text files include normalized total count values for each Sample

source_name: TAMs from LLC tumors of miR-21 null mouse

growth_protocol: LLC cells were subcutaneously implated in WT or miR-21 null mice. After 14 days tumors were isolated digested and TAMs  were FACS sorted as (CD45+, CD11b+, MHCII+, F4/80+)

extract_protocol:
Total RNA for sorted TAMs isolated form LLC tumors implated in WT or mir-21 null mice was extracted using Rneasy Micro Kit (cat no 74004, Qiagen, Venlo, Netherlands). Briefly: sorted TAMs were resuspended in the lysis buffer provided by the kit and following ethanol washes and genomic DNA digestion RNA was eluted.
The Kapa mRNA Hyper prep kit (Cat# KK8581) was used. The Kapa DI Adapter Kit (Cat# KK8722) was used for the indexes.

value: tumor associated macrophages

value: 10 weeks

tag: genotype

value: miR-21 null


title: wt

description: 3 pooled biological replicates

source_name: CD45 cells pooled from LLC tumors of  3 mir-21flox/flox; mir21 flox/flox ( conditional ko -=cko) mice


title: HNF-1β KO Mock RNA-seq Rep1

description:
HNF1bKO-Mock_1
HNF-1β -/-
processed data file: subread.txt

tag: treatment


title: NT2/D1-H1_rep3

description:
processed data file: NT2_GEO_Processed.txt
NT2_H1_UT_3_GGCTTAAG-TCGTGACC_L00M

source_name: Derived from NT2/D6


title: NT2/D1-H1_rep1

description:
processed data file: NT2_GEO_Processed.txt
NT2_H1_UT_1_CCAAGTCT-AAGGATGA_L00M

source_name: Derived from NT2/D4


title: miRKO3

description:
Biological Replicate 2
miRKO3_GAATTCGT


title: miRWT4

description:
Biological Replicate 4
miRWT4_GAGATTCC

source_name: TAMs from LLC tumors of WT mouse


title: NT2/D1-C2_rep1

description:
processed data file: NT2_GEO_Processed.txt
NT2_C2_UT_1_CAAGCTAG-ACATAGCG_L00M

source_name: Derived from NT2/D1


title: miRKO4

description:
Biological Replicate 3
miRKO4_CTGAAGCT


title: miRKO1-2

description:
Biological Replicate 1
miRKO1-2_ATTCAGAA


title: HNF-1β KO Wnt3a RNA-seq Rep3

description:
HNF1bKO-Wnt3A_3
HNF-1β -/-
processed data file: subread.txt


title: NT2/D1-C2_rep2

description:
processed data file: NT2_GEO_Processed.txt
NT2_C2_UT_2_TGGATCGA-GTGCGATA_L00M

source_name: Derived from NT2/D2


title: NT2/D1-C2_rep3

description:
processed data file: NT2_GEO_Processed.txt
NT2_C2_UT_3_AGTTCAGG-CCAACAGA_L00M

source_name: Derived from NT2/D3


title: NT2/D1_rep5

description:
processed data file: NT2_GEO_Processed.txt
NT2_9_15_UT_2_TTATAACC-GATATCGA_L00M

source_name: Cell lines From ATCC


title: NT2/D1_rep6

description:
processed data file: NT2_GEO_Processed.txt
NT2_9_15_UT_3_GGACTTGG-CGCAGACG_L00M


title: 2102EP-A1_rep3

description:
processed data file: EP_GEO_Processed.txt
2102EP_A1_UT_3_ATGGCATG-AAGGTACC_L00M


title: HNF-1β KO Mock RNA-seq Rep3

description:
HNF1bKO-Mock_3
HNF-1β -/-
processed data file: subread.txt

source_name: mIMCD3 cells


title: miRWT2

description:
Biological Replicate 2
miRWT2_TCCGGAGA


title: miRWT1

description:
Biological Replicate 1
miRWT1_ATTACTCG


title: NT2/D1_rep4

description:
processed data file: NT2_GEO_Processed.txt
NT2_9_15_UT_1_CCGCGGTT-AGCGCTAG_L00M


title: NT2/D1-B3_rep3

description:
processed data file: NT1_GEO_Processed.txt
NT2B3_UT3_ATTCAGAA-TATAGCCT_L00M


title: 2102EP_rep2

description:
processed data file: EP_GEO_Processed.txt
2102EP_UT_2_CTACGACA-GAGTCCAA_L00M


title: NT2/D1-B3_rep2

description:
processed data file: NT1_GEO_Processed.txt
NT2B3_UT2_GAGATTCC-GTACTGAC_L00M


title: NT2/D1-B3_rep1

description:
processed data file: NT1_GEO_Processed.txt
NT2B3_UT1_GAGATTCC-CAGGACGT_L00M


title: NT2/D1-A4_rep3

description:
processed data file: NT1_GEO_Processed.txt
NT2A4_UT3_TCCGGAGA-CAGGACGT_L00M


title: NT2/D1-A4_rep2

description:
processed data file: NT1_GEO_Processed.txt
NT2A4_UT2_TCCGGAGA-TAATCTTA_L00M


title: NT2/D1-A4_rep1

description:
processed data file: NT1_GEO_Processed.txt
NT2A4_UT1_TCCGGAGA-AGGCGAAG_L00M


title: miRWT3

description:
Biological Replicate 3
miRWT3_CGCTCATT


title: NT2/D1-A3_rep3

description:
processed data file: NT1_GEO_Processed.txt
NT2A3_UT3_TCCGGAGA-TATAGCCT_L00M


title: NT2/D1-A3_rep1

description:
processed data file: NT1_GEO_Processed.txt
NT2A3_UT1_ATTACTCG-CAGGACGT_L00M


title: Patient X - positively sorted for CLEC14A

city: Berlin

first: Nikos

last: Karaiskos

address: Hannoversche Str. 28

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description:
rRNA depleted RNA
Bulk RNA-seq

data_processing:
Single-cell sequenced reads were converted to SAM files to couple them with the cell and molecular barcodes using Drop-seq_tools v1.12. They were further trimmed for SMART adapter and poly(A) remnants.
The filtered reads were mapped with STAR. The Drop-seq_tools v.1.12 were used to add gene annotations, detect bead synthesis errors and calculate the Digital Gene Expression matrices.
Pre-processed raw RNA-Seq data were mapped using CLC Genomics Workbench (v. 12) with a workflow executing the following the steps: (1) quality read trimming using quality score <10 (2) quality control (3) RNA-Seq analysis by aligning reads to the human reference genome and transcriptome (GRCh38).
Genome_build: GRCh38
Supplementary_files_format_and_content: BulkRNAseq: Tab-delimeted text files include read-counts and CPM, TPM, RPKM values

source_name: Human Primary Myoblasts

growth_protocol: Muscle biopsy specimens for myoblast isolation were obtained from M. vast. lat. after IRB approval (EA1/203/08 and EA2/051/10). Myoblast isolation was performed as described. (Marg et al., 2012) Contamination of myoblast cultures with fibroblasts was always below 5%. Myoblasts were seeded and grown in skeletal muscle growth medium (ProVitro, Germany) until they reached 50-60% confluence.

extract_protocol:
Total RNA was isolated from human primary myoblasts using NucleoSpin® RNA/Protein Kit (Marcherey-Nagel, Germany) and treated with DNAse for genomic DNA removal. RNA quantity and purity were determined with a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, USA). RNA quality was evaluated using TapeStation (Agilent Technologies, USA). The RIN factor was >8 for all samples.
cDNA libraries from rRNA depleted RNA for 75nt single-end sequencing were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina sequencing (NEB, USA). RNA sequencing was performed at Illumina MiSeq platform (Illumina, USA).
Bulk RNA-seq

tag: passage number

tag: type of muscle

value: M vast lat

tag: donor age (y)

tag: donor gender

value: male

tag: pax7 positive myoblasts


title: Patient U - positively sorted for CLEC14A

description:
rRNA depleted RNA
Bulk RNA-seq


title: Patient U - negatively sorted for CLEC14A

description:
rRNA depleted RNA
Bulk RNA-seq


title: NT2/D1-A3_rep2

description:
processed data file: NT1_GEO_Processed.txt
NT2A3_UT2_ATTACTCG-GTACTGAC_L00M

tag: cell type


title: NT2/D1_rep3

description:
processed data file: NT1_GEO_Processed.txt
NT21_21_17_UT3_CGCTCATT-AGGCGAAG_L00M

source_name: Testicular embryonal carcinoma cell lines derived from metastatic site, Lung


title: Patient T - PAX7 negative myoblast population

description:
rRNA depleted RNA
Bulk RNA-seq

value: female


title: NT2/D1-H1_rep2

description:
processed data file: NT2_GEO_Processed.txt
NT2_H1_UT_2_TTGGACTC-GGAAGCAG_L00M

source_name: Derived from NT2/D5


title: NT2/D1_rep1

description:
processed data file: NT1_GEO_Processed.txt
NT21_21_17_UT1_CGCTCATT-CCTATCCT_L00M

source_name: Testicular embryonal carcinoma cell lines derived from metastatic site; Lung


title: Patient T - PAX7 positive myoblast population

description:
rRNA depleted RNA
Bulk RNA-seq


title: Patient Q - PAX7 negative myoblast population

description:
rRNA depleted RNA
Bulk RNA-seq


title: Patient Q - PAX7 positive myoblast population

description:
rRNA depleted RNA
Bulk RNA-seq


title: Adult cardiomyocyte WT with Iso treatment, biological rep1

type: RNA

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Gene expression data from adult cardiomyocytes isolated form CaMKII-WT with ISO stimulation

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Adult mouse ventricular myocytes (AMVMs) from double knockout mice deficient for CaMKIIδ and CaMKIIγ (CaMKII DKO) or corresponding wild type (WT) mice were enzymatically Isolated using the Langendorff perfusion system.

extract_protocol:
Total RNA was isolated from cultured cardiomyocytes using trizol
reagent procedure (Life technologies).

treatment_protocol: Isolated adult cardiomyocytes from CaMKII-WT or DKO mice were stimulated with or without 100 nM Iso for  24 h.

tag: mouse id#

value: adult

tag: genetic information

value: wild type (WT)

value: 100 nM ISO for  24 h


title: Adult cardiomyocyte WT with Iso treatment, biological rep2

value: Adult mouse ventricular myocytes (AMVMs)


title: Adult cardiomyocyte WT with Iso treatment, biological rep3


title: Adult cardiomyocyte DKO with Iso treatment, biological rep2

description: Gene expression data from adult cardiomyocytes isolated form CaMKII-DKO with ISO stimulation

value: double knockout mice deficient for CaMKIIδ and CaMKIIγ (CaMKII DKO)


title: Adult cardiomyocyte DKO with Iso treatment, biological rep3


title: colorectal cancer sample AUS2_647

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

description:
RMA expression values at the gene-level derived using the justRMA algorithm implemented in the R package affy with custom CDF file from Brainarray (version 22 GENECODEG)
AUS2_647_p5264

hyb_protocol: Samples were hybridized onto Affymetrix Human Transcriptome 2.0 Arrays according to the manufacturer's protocol (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's protocol (Affymetrix).

data_processing: The re-analyzed GSMs include two Affymetrix platforms, HTA-2_0 and HuEx-1_0-st.  Re-normalization was performed separately for each platform and the data matrices are included on the series record.  Gene-level expression signals were obtained from raw data CEL files by the RMA procedure using the justRMA algorithm implemented in the R package affy with custom CDF file from Brainarray (version 22 GENECODEG) for each platform. GPL27634 is the platform for the GENECODEG v 22 HTA-2_0 array and GPL27639 is the platform for the GENECODEG v 22 HuEx-1_0-st array.

source_name: Colorectal cancer patient

label_protocol: RNA was amplified, fragmented and labelled according to the Affymetrix GeneChip HT WT User Guide.

extract_protocol: Total RNA was isolated from colorectal cancer tissue samples using the Qiagen Allprep DNA/RNA/miRNA Universal kit, according to the manufacturer's protocol (Qiagen).

value: colorectal cancer tissue sample


title: Adult cardiomyocyte WT, biological rep1

description: Gene expression data from adult cardiomyocytes isolated form CaMKII-WT without ISO stimulation

source_name: Adult cardiomyocyte WT

value: Ctrl


title: Adult cardiomyocyte WT, biological rep2


title: colorectal cancer sample AUS2_618

description:
RMA expression values at the gene-level derived using the justRMA algorithm implemented in the R package affy with custom CDF file from Brainarray (version 22 GENECODEG)
AUS2_618_p5234


title: Adult cardiomyocyte WT, biological rep3


title: CON-2

city: Shanghai

first: Gao

last: Ya

state: Shanghai

address: Zhizaoju road No.639

department: School of medicine

country: China

institute: Shanghai Jiao Tong University

data_processing:
RNA quantity and quality were measured using a NanoDrop ND-1000. The cDNA library was constructed using KAPA Stranded RNA-Seq Library Preparation Kit (Illumina) following the manufacturer’s protocol.
The final double-stranded cDNA samples were verified with an Agilent 2100 Bioanalyzer (Agilent Technologies).
After cluster generation (TruSeq SR Cluster Kit v3-cBot-HS, Illumina), sequencing was performed on an Illumina HiSeq 4000 sequencing platform.
Image analysis, base calling, and error estimation were performed using Illumina/Solexa Pipeline version 1.8 (Off-Line Base Caller software, version 1.8).
Raw data were pre-processed using Solexa CHASTITY and Cutadapt to remove adaptor sequences, ribosomal RNA, and other contaminants that may interfere with clustering and assembly. The trimmed reads are mapped to the corresponding reference genome using HISAT2 (version 2.0.4) for RNA-seq, and StringTie (version 1.2.3) was used to reconstruct the transcriptome.
Genome_build: hg19
Supplementary_files_format_and_content: Expression_Gene.xlsx inclucing: Track_ID :  Gene_Name : Locus :  Strand : Gene_Type :  etc.

source_name: HaCaT cells

growth_protocol: HaCaT cell line was purchased from the ATCC (American Type Culture Collection) and was cultured in Gibco™ RPMI 1640 and 10% fetal bovine serum, supplemented with antibiotics (penicillin 100 IU/mL and streptomycin 100 mg/mL) in 5% CO2at 37 °C.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After HaCaT reach 80%  confluence, recombined human LRG1 diluted in PBS was added(500ng/ml, 12h) ,the control group added same volume PBS.

value: HaCaT cells (immortal keratinocyte cell line)

tag: passages

tag: strain

value: human


title: colorectal cancer sample AUS2_629

description:
RMA expression values at the gene-level derived using the justRMA algorithm implemented in the R package affy with custom CDF file from Brainarray (version 22 GENECODEG)
AUS2_629_p5246

tag: tissue


title: PAX7null_bulk: Patient with homozygous PAX7 splicing mutation and PAX7 deficient myoblasts

data_processing:
Demultiplexed raw RNA-Seq data were imported and mapped using CLC Genomics Workbench (v. 9.5) with a workflow executing the following the steps: (1) quality read trimming using quality score <10 (2) quality control (3) RNA-Seq analysis by aligning reads to the human reference genome and transcriptome (GRCh38).
processed data files format and content: Tab-delimeted text files include read-counts and simple fold change data relative to PAX7-I
Genome_build: GRCh38

extract_protocol:
Total RNA was isolated from human primary myoblasts using NucleoSpin® RNA/Protein Kit (Marcherey-Nagel, Germany) and treated with DNAse for genomic DNA removal. RNA quantity and purity were determined with a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, USA). RNA quality was evaluated using TapeStation (Agilent Technologies, USA). The RIN factor was >9 for all samples.
cDNA libraries from rRNA depleted RNA for 75nt paired-end sequencing were prepared using the NEBNext® rRNA Depletion Kit and NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina sequencing (NEB, USA). RNA sequencing was performed at Illumina MiSeq platform (Illumina, USA).

value: human primary myoblasts cell line

tag: donor age (yrs)

tag: gender

tag: genotype/variation

value: Splicing mutation in Intron 1

tag: method

value: Bulk RNA-seq


title: Adult cardiomyocyte DKO with Iso treatment, biological rep1

tag: age


title: PAX7pos-I_bulk: Donor I - PAX7 positive myoblast population

tag: cell line


title: CON-1


title: LRG1-2


title: NT2/D1_rep2

description:
processed data file: NT1_GEO_Processed.txt
NT21_21_17_UT2_CGCTCATT-GGCTCTGA_L00M

value: Embryonic carcinoma

tag: tissue origin

value: testis

tag: cisplatin sensitivity

value: Cisplatin sensitive


title: MmDG-Sox11-5

status: Public on Nov 10 2019

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

institute: Uniklinikum Erlangen

description: normcounts.txt

data_processing:
Basecalling and demultiplexing were performed using the software provided by Illumina (RTA 1.18.66.3, bcl2fastq 1.8.4)
Filtering was performed using cutadapt v. 1.9.1.
Reads were mapped against the GRCm38 mouse reference genome using the STAR aligner v. 2.5.2a
Read counts per gene were obtained using the subRead featureCounts program v. 1.5.1 (Liao 2014) and the Ensembl gtf annotation file.
Differential expression analysis was performed with the DESeq2 package v.1.12.3 using R version 3.3.1.
Genome_build: Ensembl GRCm38.85
Supplementary_files_format_and_content: tab-separated text with normalized count data (DESeq2)

source_name: Dentate gyrus

growth_protocol: Mice were housed under a 12 h light/dark cycle with ad libidum access to food and water. We used 8-weeks old mice in RNA-Seq experiments.

extract_protocol:
The dentate gyrus (DG) was microdissected from unfixed brain tissue. Mice were killed by cervical dislocation and the DG was dissected as described (Hagihara, Toyama et al. 2009). The prepared tissue was stored in stabilizing RNAlater buffer (Qiagen, Cat No./ID: 76154) until RNA was isolated using the RNeasy Kit (Qiagen, Cat No./ID: 74106) according to manufacturer’s instructions.
Barcoded RNA sequencing libraries were prepared from 100 ng total RNA using TruSeq Stranded mRNA Sample Preparation Kit, according to the manufacturer’s instructions (Illlumina).

treatment_protocol: 1µl virus solution of Adeno-associated viruses (AAV) Serotype 9 encoding either for GFP or for Sox11 was injected into the left and right dentate gyrus (coordinates from bregma: ±1.6 mm medial/lateral, -1.9 mm anterior/posterior, -1.9 mm ventral/dorsal from brain surface).

tag: transduction

value: 8 weeks


title: MmDG-Sox11-3

description: normcounts.txt


title: MmDG-Sox11-4

description: normcounts.txt


title: Patient with homozygous PAX7 splicing mutation and PAX7 deficient myoblasts

description:
rRNA depleted RNA
Bulk RNA-seq

tag: passage number

tag: type of muscle

value: M vast lat

tag: donor age (y)

tag: donor gender

value: female

tag: genotype


title: PAX7neg-B_bulk: Donor B - PAX7 negative myoblast population

tag: cell type

tag: pax7 positive myoblasts


title: MmDG-GFP-3

description: normcounts.txt

tag: strain

value: GFP


title: MmDG-GFP-2

description: normcounts.txt


title: MmDG-GFP-1

description: normcounts.txt


title: MmDG-Sox11-1

description: normcounts.txt


title: MmDG-GFP-4

description: normcounts.txt


title: B16_PD1_1

city: Philadelphia

first: Zilu

last: Zhou

address: 3730 Walnut St

institute: University of Pennsylvania

description: B16 cell line injected on flanks, treated with anti-PD1 on Days 5,8, and 11, harvested on Day 15

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Raw fastq file was aligned by STAR 2-pass method (default parameters), which accounts for splicing junctions and achieve higher mapping quality
Transcripts per million (TPM) was quantified using RSEM (default parameters)
Raw variants calling is made using the Haplotype Caller (GATK tool) on the BAM files after sorting, joining read groups, removing duplicated reads, removing overhangs into intronic regions, realigning and recalibratio
Genome_build: mm10
Supplementary_files_format_and_content: CSV contains expression value of each single cell (row) across genes (column) in TPM unit

growth_protocol: 50,000 tumor cells were injected subcutaneously on Day 0. Tumor cells were sorted on Day 15.

extract_protocol:
Sorted cells were loaded on ICELL8 platform
SMARTer ICELL8 SMART-Seq protocol was used to obtain libraries of full length transcripts
Single Cell RNA-sequencing

treatment_protocol: Two of the mice implanted with B16 were treated with 200 ug of anti-PD1 per mouse on Days 5, 8 and 11.

tag: treatment

value: Treated with 200 ug of PD1 on Days 5, 8 and 11

tag: library construction

value: Smart-seq


title: Adult cardiomyocyte DKO, biological rep3

description: Gene expression data from adult cardiomyocytes isolated form CaMKII-DKO without ISO stimulation

source_name: Adult cardiomyocyte DKO

tag: mouse id#

value: adult

tag: genetic information

value: double knockout mice deficient for CaMKIIδ and CaMKIIγ (CaMKII DKO)

value: Adult mouse ventricular myocytes (AMVMs)


title: B16_2

description: B16 cell line injected on flanks harvested on Day 15

value: Untreated


title: R499_1

description: R499 cell line injected on flanks harvested on Day 15

source_name: B16-F10 derived Res499


title: MmDG-GFP-5

description: normcounts.txt

tag: age


title: Adult cardiomyocyte DKO, biological rep2

value: Ctrl


title: Resveratrol 10 min replicate 2

city: Madrid

first: Felix

last: Lopez de Felipe

address: Jose Antonio Novais

country: Spain

institute: ICTAN-CSIC

description:
Biological replicate 2 of 3
Slide L. plantarum WCFS1 8x15K microarray GE Agilent G2509F Oligo Microarrays No. 026636 was custom designed and contains 60-mer probes that were taken at the gene expression omnibus database (GEO accession number GLP5874). The oligo-microarray contained an average of three probes per transcript. Each slide contains 8 arrays, these are numbered as follows: 1_1 (1st column upper row), 1_2 (2nd column upper row), 1_3 (3rd column upper row), 1_4 (4th column upper row),  2_1 (1st column lower row),2_2 (2nd column lower row), 2_3 (3rd column lower row), 2_4 (4th column lower row).

hyb_protocol: Preparation of probes and hybridization was performed as described on the Two-Color Microarray Based Gene Expression Analysis Manual (Quick Amp Labeling) with Tecan HS Pro Hybridization (Ver. 5.7/Agilent Technologies): for each hybridization 300 ng of Cy3 and HyPer5 probes were added to 5 uL of 10x Blocking Agent, 1.2 uL of 25x Fragmentation Buffer and nuclease-free water to bring volume to 25 uL reaction and incubated at 60 ºC for 30 min. Then, 25 uL the 2x GEx Hybridization Buffer HI-RPM were added and loaded onto the arrays. The arrays were hybridized for 17 hours at 65ºC, and washed in GE Wash Buffer 1 and then in GE Wash Buffer 2. Finally, these were drained by centrifugation and scanned.

scan_protocol: Images were captured with a Agilent Technologies Scanner G2505C / GenePix 4000B (Axon) and spots quantified using GenPix software (Axon).

data_processing: Background correction and normalization of expression data were performed using the methods normexp and loess in LIMMA. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate p-values were corrected by using the method of Benjamani and Hochberg. The expected False Discovery Rate (FDR) was controlled to be less than 5%. Genes were considered differentially expressed when nominal p-values were <0.05 and had a fold change (FC) equal or higher than ±1.5. FC was calculated as the average of the fold change between significantly regulated probes.

organism: Lactiplantibacillus plantarum

source_name: Treated cells: Experimental

label_protocol: Fluorescently labelled cDNA for microarray hybridizations was obtained by using the SuperScript Indirect cDNA Labeling System (Invitrogen): 20 ug of total RNA was transformed to cDNA with SuperscriptTM III Reverse Transcriptase using anchored oligo(dT)20 primers, and including aminoallyl-modified nucleotides. After cDNA purification, the Cy3 and HyPer5 fluorescent dyes (Amersham Biosciences) were coupled to the aminoallyl-modified first-strand cDNA. Purification of Cy3- and HyPer5-labeled cDNA probes was carried out with the CyScribe GFX Purification Kit.

growth_protocol: Paired independent L. plantarum batch cultures (50 mL each) were grown in MRS lacking resveratrol to an OD600 ≈ 0.8-0.9, then one pair of the culture were exposed  to resveratrol to bring their final concentration to 3 mM. Cell cultures were centrifuged after 10 minutes of exposure to resveratrol and RNA was extracted and purified.

extract_protocol: For RNA extraction the celular pellet was mixed with 2 mL of quenching buffer (60% methanol, 66.7 mM HEPES, pH 6.5, -40 ºC) . Following quenching, the cells were pelleted by centrifugation at 9,000 x g for 10 min at -10 ºC, transferred to a screw cap tube containing an extraction mixture (500 uL 1:4 chloroform-acid phenol, 30uL of 10% SDS, 30uL Na-acetate 3M pH 5.2, 400uL Tris-EDTA buffer [10 mM Tris(hydroxymethyl)amino methane, 1 mM EDTA] pH 7.4, 15 mg of polyvinylpoly-pyrrolidone, and 500 mg of 75-150um glass beads). The cells were broken under frozen conditions in the Mini-BeadBeather (BIOSPEC Products, INC.) using three treatments of 4600 rpm for 40 seconds cycles (and chilled on dry ice for 60 seconds between cycles). The suspension was then centrifuged at 4 ºC at 10,000 x g for 2 min. Two extractions with 500 uL of chloroform were performed, and the supernatant containing the RNA was separated by centrifugation.  The sample was immediately frozen in liquid nitrogen, and stored at -80 ºC. NanoDrop ND-1000 instrument was used for quantification of RNA. Continued with the QUIAGEN RNA isolation kit. Two treatments with DNase I (Ambion) were applied and the absence of genomic DNA was confirmed by PCR.

tag: compound

value: Resveratrol 3mM

source_name: Untreated cells: Control

value: without resveratrol


title: R499_2


title: Resveratrol 10 min replicate 3

description:
Biological replicate 3 of 3
Slide L. plantarum WCFS1 8x15K microarray GE Agilent G2509F Oligo Microarrays No. 026636 was custom designed and contains 60-mer probes that were taken at the gene expression omnibus database (GEO accession number GLP5874). The oligo-microarray contained an average of three probes per transcript. Each slide contains 8 arrays, these are numbered as follows: 1_1 (1st column upper row), 1_2 (2nd column upper row), 1_3 (3rd column upper row), 1_4 (4th column upper row),  2_1 (1st column lower row),2_2 (2nd column lower row), 2_3 (3rd column lower row), 2_4 (4th column lower row).

treatment_protocol: Cell cultures were centrifuged after 10 minutes of exposure to resveratrol and RNA was extracted and purified.


title: B16_1


title: Adult cardiomyocyte DKO, biological rep1


title: Resveratrol 10 min replicate 1

description:
Biological replicate 1 of 3
Slide L. plantarum WCFS1 8x15K microarray GE Agilent G2509F Oligo Microarrays No. 026636 was custom designed and contains 60-mer probes that were taken at the gene expression omnibus database (GEO accession number GLP5874). The oligo-microarray contained an average of three probes per transcript. Each slide contains 8 arrays, these are numbered as follows: 1_1 (1st column upper row), 1_2 (2nd column upper row), 1_3 (3rd column upper row), 1_4 (4th column upper row),  2_1 (1st column lower row),2_2 (2nd column lower row), 2_3 (3rd column lower row), 2_4 (4th column lower row).


title: NEO1–Hoxb5+ LT-HSCs [Sample5]

city: Palo Alto

first: Gunsagar

middle: Singh

last: Gulati

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

description: mRNA

data_processing:
Bcl2fastq2 v2.18 (Illumina) was used to extract the data and generate FASTQ files for each sample by using unique barcode combinations from the Nextera preparation
Raw reads were trimmed for base call quality (PHRED score >=21) and for adapter sequences using Skewer v0.2.2 with default settings
Trimmed reads were then aligned to the mouse genome assembly (mm10) from UCSC (http://genome.ucsc.edu) using STAR v2.4 with default setting
Raw counts from STAR v2.4 were inputted into a DESeqDataSet (DESeq2 v1.22.2 package in R) object indicating NEO1 status (‘status’) and mouse subject (‘subject’) as factors (‘design = ~subject + status’). Counts were then size-factor normalized using the ‘DESeq’ function and log2-transformed.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include (1) raw read count values for each sample (2) size factor- and log-normalized count values for each sample

source_name: Bone marrow

extract_protocol:
250-500 cells from two pooled mice per sample were sorted directly into 100 μL of lysis buffer (Buffer RL) and RNA was isolated with the Single Cell RNA Purification Kit (Norgen Biotek Corp.) according to the manufacturer’s protocol. RNA quality was measured by capillary electrophoresis using the Agilent 2100 Bioanalyzer with Nano mRNA assay at the Stanford Protein and Nucleic Acid (PAN) Facility
Libraries were prepared using the Smart-seq2 protocol by Picelli et al., 2014 with minor modifications. Briefly, cDNA was generated by oligo-dT primed reverse transcription with MMLV reverse transcriptase (SMARTScribe, Clontech) and a locked template-switching oligonucleotide (TSO). This was followed by 18 cycles of PCR amplification using KAPA HiFi hotStart ReadyMix and ISPCR primers. Amplified cDNA was then purified using 0.7x volume Agencourt AMPure XP beads to remove smaller fragments. The resulting cDNA concentration and size distribution for each well was determined on a capillary electrophoresis-based Agilent 2100 Bioanalyzer with High Sensitivity DNA chip at the Stanford PAN facility. 40 ng of cDNA was then tagmented, uniquely barcoded, and PCR enriched using the Nextera DNA Library Prep Kit (Illumina, San Diego, CA). Libraries were then pooled in equimolar amounts and purified of smaller fragments using 0.7x Agencourt AMPure XP beads. Pooled libraries were checked for quality using the Agilent Bioanalyzer with High Sensitivity DNA chip at the Stanford PAN facility.

tag: tissue

value: bone marrow

tag: gating strategy

value: Lin- cKIT+ SCA1+ CD150+ CD48- FLK2- CD34- Hoxb5+ NEO1-


title: NEO1–Hoxb5+ LT-HSCs [Sample3]

description: mRNA


title: NEO1–Hoxb5+ LT-HSCs [Sample4]

description: mRNA


title: NEO1–Hoxb5+ LT-HSCs [Sample2]

description: mRNA


title: MmDG-Sox11-2

description: normcounts.txt

tag: transduction


title: NEO1–Hoxb5+ LT-HSCs [Sample1]

description: mRNA


title: NEO1+Hoxb5+ LT-HSCs [Sample3]

description: mRNA

value: Lin- cKIT+ SCA1+ CD150+ CD48- FLK2- CD34- Hoxb5+ NEO1+


title: NEO1+Hoxb5+ LT-HSCs [Sample4]

description: mRNA


title: NEO1+Hoxb5+ LT-HSCs [Sample5]

description: mRNA


title: B16_PD1_2


title: NEO1+Hoxb5+ LT-HSCs [Sample1]

description: mRNA


title: LRG1-1

value: HaCaT cells (immortal keratinocyte cell line)

tag: passages

value: human


title: HPV16 wt rep3

city: Shreveport

first: Rona

middle: S.

last: Scott

state: LA

address: 1501 Kings Highway

department: Microbiology and Immunology

institute: Louisiana State University Health Sciences Center-Shreveport

data_processing:
Base calling and quality scoring were performed with Ilumina Real Time Analysis software (RTA v2.4.11)
Reads with quality scores above 30 were aligned using STAR_2.4.2a to human (GrCh38p10) and HPV16 (NC_001526.3)
The Transcripts per million (TPM) were calculated using RSEM 1.2.31
Reads with TPM > 1 in at least 1 out of 6 replicated samples were included for downstream analysis
Genome_build: human (GrCh38p10, HPV16 (NC_001526.3)
Supplementary_files_format_and_content: TPM

source_name: human foreskin primary keratinocytes_HPV16 WT

growth_protocol: Primary keratinocytes infected for 5-7days with HPV16 wt or E7-TTL mutant virus as well as uninfected cotrol cells were subjected to organotypic raft culture for 21 days.

extract_protocol:
RNA from raft tissues was extracted using the Qiagen QIAcube via the miRNeasy aqueous-phase protocol.
Strand specific mRNA-seq libraries for the Illumina platform were prepared using the NEBNextUltra directional library kit (NEB) and the TruSeq stranded mRNA kit (Illumina).

tag: tissue source

value: foreskin

value: primary keratinocytes

tag: infection

value: HPV16 WT

tag: culture condition

value: 3D raft culture


title: HPV16 wt rep2


title: CTRL rep3

source_name: human foreskin primary keratinocytes_uninfected control

value: uninfected control


title: NEO1+Hoxb5+ LT-HSCs [Sample2]

description: mRNA


title: HPV16 E7TTL rep1

source_name: human foreskin primary keratinocytes_HPV16 E7-TTL

value: HPV16 E7-TTL


title: HPV16 E7TTL rep2


title: CTRL rep1


title: CTRL rep2


title: HPV16 WT 43-63dpi Y- rep3 [P8_TPM]

data_processing:
Base calling and quality scoring were performed with Ilumina Real Time Analysis software (RTA v2.4.6.0 and v2.4.11)
Reads with quality scores above 30 were aligned using STAR_2.4.2a to human (GrCh38p10) and HPV16 (NC_001526.3)
The Transcripts per million (TPM) were calculated using RSEM 1.2.31
Reads with TPM > 1 in at least 1 out of 6 replicated samples were included for downstream analysis
Genome_build: human (GrCh38p10), HPV16 (NC_001526.3)
Supplementary_files_format_and_content: TPM

source_name: HPV16 WT 43-63dpi Y-

growth_protocol: Control and HPV16-infected or HPV-immortalized cells were grown in a monolayer culture in E medium and mytomycin-treated mouse 3T3 J2 feeders cells.

extract_protocol:
Cells were trypsinized and RNA was harvested using Trizol reagent (sample 1-12) or using the RNeasy Plus Mini RNA Isolation Kit (samples 13-30) (Qiagen; 74236).
Strand specific mRNA-seq libraries for the Illumina platform were prepared using the NEBNextUltra directional library kit (NEB) and the TruSeq stranded mRNA kit (Illumina).

value: 43-63 dpi with HPV16 WT

value: mouse EGF


title: HPV16 WT 43-63dpi Y- rep2 [O8_TPM]


title: CTRL rep4


title: HPV16 wt 36-55dpi Y- rep3 [P7_TPM]

source_name: HPV16 wt 36-55dpi Y-

value: 36-55 dpi with HPV16 WT


title: CTRL rep5


title: HPV16 E7TTL rep3


title: HPV16 wt rep5


title: HPV16 WT 43-63dpi Y- rep1 [N8_TPM]


title: HPV16 wt 36-55dpi Y- rep2 [O7_TPM]


title: HPV16 E7TTL rep5


title: HPV16 wt 36-55dpi Y- rep1 [N7_TPM]


title: YE_8-3-3

city: San Francisco

first: Meena

last: Subramaniam

address: 513 Parnassus Ave S-965

institute: UCSF IHG

description: sle.mtx

data_processing:
10x CellRanger was run on each faw sample with default settings
Demuxlet software was run on each sample with default settings and genotyping parameter 0.1
Counts matrices  from the 10x Cellranger software were aggregated across samples and doublets flagged by Demuxlet were removed
Genome_build: hg19
Supplementary_files_format_and_content: MTX files (count matrices), TXT files (row and column annotations)

source_name: Peripheral blood mononuclear cells

extract_protocol:
PBMCs from SLE patients and healthy controls were Ficoll-isolated and prepared using the 10x Chromium Single cell instrument standard protocol.
10x Chromium Single Cell Workflow
10x Chromium Single Cell Library Prep

value: PBMCs

tag: condition

value: SLE

tag: sample type

value: primary cells

tag: chip antibody


title: YE_8-9-4

description: sle.mtx

tag: cell type


title: YE_8-3-2

description: sle.mtx


title: YE_8-9-3

description: sle.mtx


title: YE_8-3-4

description: sle.mtx


title: HPV16 E7TTL 27-33dpi Y- rep3 [P6_TPM]

source_name: HPV16 E7TTL 27-33dpi Y-

value: 27-33 dpi with HPV16 E7-TTL


title: YE_8-3-1

description: sle.mtx


title: HPV16 E7TTL rep4


title: YE_8-2-4

description: sle.mtx


title: YE_8-2-3

description: sle.mtx


title: HPV16 wt 27-33dpi Y- rep3 [P4_TPM]

source_name: HPV16 wt 27-33dpi Y-

value: 27-33 dpi with HPV16 WT


title: HPV16 E7TTL 27-33dpi Y- rep1 [N6_TPM]


title: YE_8-23-3

description: sle.mtx


title: HPV16 wt rep1


title: YE_8-23-2

description: sle.mtx


title: YE_8-23-4

description: sle.mtx


title: YE_8-23-1

description: sle.mtx


title: CTRL 27-33dpi  Y- rep3 [P3_TPM]

source_name: CTRL 27-33dpi  Y-

value: 27-33 d ECM only


title: YE_8-2-1

description: sle.mtx


title: YE_8-2-2

description: sle.mtx


title: HPV16 wt 27-33dpi Y- rep1 [N4_TPM]


title: CTRL 27-33dpi  Y- rep1 [N3_TPM]


title: HPV16 E7TTL 27-33dpi Y- rep2 [O6_TPM]


title: CTRL 27-33dpi  Y- rep2 [O3_TPM]


title: YE_8-17-4

description: sle.mtx


title: HPV16 IMMORT Y+ rep3 [S3_TPM]

source_name: HPV16 IMMORT Y+

value: transfected/immortalized with HPV16 genome

value: with ROCK inhibitor (Y-27632)


title: YE_8-17-3

description: sle.mtx


title: HPV16 IMMORT Y+ rep2 [S2_TPM]

value: foreskin


title: HPV16 IMMORT Y- rep2 [H1_TPM]

source_name: HPV16 IMMORT Y-

value: primary keratinocytes


title: HPV16 IMMORT Y- rep3 [I1_TPM]


title: HPV16 IMMORT Y- rep1 [G1_TPM]


title: YE_8-16-4

description: sle.mtx


title: HPV16 wt 27-33dpi Y- rep2 [O4_TPM]


title: HPV16 IMMORT Y+ rep1 [S1_TPM]


title: YE_8-17-2

description: sle.mtx


title: YE_8-16-2

description: sle.mtx


title: HPV16 WT 7dpi Y+ rep2 [B4_TPM]

source_name: HPV16 WT 7dpi Y+

value: 7dpi with HPV16


title: HPV16 WT 7dpi Y+ rep1 [A4_TPM]


title: YE_7-26-4

description: sle.mtx


title: HPV16 WT 7dpi Y+ rep3 [C4_TPM]


title: CTRL Y+ rep3 [C1_TPM]

source_name: CTRL Y+

value: 7d ECM only


title: YE_7-26-3

description: sle.mtx


title: YE_7-26-1

description: sle.mtx


title: CTRL Y- rep3 [F1_TPM]

source_name: CTRL Y-

value: ECM only


title: CTRL Y+ rep1 [A1_TPM]


title: YE_7-20-4

description: sle.mtx


title: YE_8-17-1

description: sle.mtx


title: YE_7-20-3

description: sle.mtx


title: CTRL Y- rep2 [E1_TPM]


title: YE_7-20-2

description: sle.mtx


title: YE_7-20-1

description: sle.mtx


title: CTRL Y- rep1 [D1_TPM]


title: YE_8-16-3

description: sle.mtx


title: YE_7-19-4

description: sle.mtx


title: YE_7-19-3

description: sle.mtx


title: YE_7-19-2

description: sle.mtx


title: YE_8-16-1

description: sle.mtx


title: YE_7-19-1

description: sle.mtx


title: YE_7-13-4

description: sle.mtx


title: YE_7-26-2

description: sle.mtx


title: YE_7-13-2

description: sle.mtx


title: YE_7-13-1

description: sle.mtx


title: PDA15d

city: Yangling

first: bo

last: wang

state: Shaanxi

address: No. 3 Taicheng Road

institute: Northwest A&F University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Peltaster frucitcola whole genome (GenBank accession no. GCA_001592805.1) using TopHat v. 2.1.0 with parameters --bowtie1 -p 8 -g 1
A gene expression profile was created using cufflinks software.
Normalized read counts of transcripts with a significant P-value (< 0.05) and a greater than threefold change (log2) in transcript level were considered to be differently expressed. All P-values were corrected for false discoveries resulting from multiple hypothesis testing using the Benjamini-Hochberg procedure.
Genome_build: reference genome deposited at DDBJ/EMBL/GenBank under the accession GCA_001592805.1
Supplementary_files_format_and_content: tab-delimited text files include normalized read count values for each treatment.

organism: Peltaster fructicola

source_name: mycelium

extract_protocol:
Total RNA was extracted according to the instruction manual of the Trizol Reagent (Life technologies, California, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: mycelium

tag: treatment

value: potato dextrose for 15days


title: DT15d

value: mycelium on apple surface for 15days


title: YE110-4

description: sle.mtx


title: YE110-3

description: sle.mtx


title: immvarYE_8-30_3

description: sle.mtx

value: healthy


title: CTRL Y+ rep2 [B1_TPM]

value: mouse EGF


title: HPV16 wt rep4

value: HPV16 WT

value: 3D raft culture


title: JHOC5 IL-6 KD#58 replicate c

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

description: Gene expression data from cell culture

hyb_protocol: cRNA was hybridized onto chips for 18 h at 45 degrees C.  GeneChips were washed in the Affymetrix Fluidics Station 450 using the EukGE-WS2v4_450 wash protocol.

scan_protocol: Chips were scanned in an Affymetrix 3000 (7G) Confocal Scanner.

data_processing: The data were analyzed with Genespring 14.9.1 (Agilent) using Affymetrix default analysis settings (RMA processing), chips were normalized to 50th percentile, and genes were normalized to average NT values (samples #)

source_name: JHOC5 cells infected with IL-6 knockdown virus #58 replicate c

label_protocol: This project used the GeneChip™ Human Transcriptome Array 2.0 200 ng of total RNA was used as input

growth_protocol: JHOC9 cells were maintained in DMEM/F12 (Gibco, Invitrogen) supplemented with 20% fetal bovine serum (FBS) (Gemini Bio-Products, Sacramento, CA, USA). JHOC5 cells were maintained in DMEM/F12 (Gibco, Invitrogen) supplemented with 10% fetal bovine serum (FBS) (Gemini Bio-Products, Sacramento, CA, USA)

extract_protocol: Phenol/Chloroform

treatment_protocol: Effect of gene knockdown

value: Ovarian clear cell carcinoma

tag: cell line


title: JHOC5 IL-6 KD#58 replicate b

description: Gene expression data from cell culture

source_name: JHOC5 cells infected with IL-6 knockdown virus #58 replicate b


title: JHOC5 SPINK1 KD #9 replicate d

description: Gene expression data from cell culture

source_name: JHOC5 cells infected with SPINK1 knockdown virus #9 replicate d


title: immvarYE_8-30_1

description: sle.mtx

value: PBMCs

value: primary cells


title: immvarYE_8-30_2

description: sle.mtx


title: JHOC5 NT (control) Experiment E replicate e

description: Gene expression data from cell culture

source_name: JHOC5 cells infected with NT control lentivirus experiment E replicate e


title: YE110-2

description: sle.mtx

value: SLE


title: JHOC5 NT (control) Experiment D replicate d

description: Gene expression data from cell culture

source_name: JHOC5 cells infected with NT control lentivirus experiment D replicate d


title: JHOC5 SPINK1 KD #9 replicate c

description: Gene expression data from cell culture

source_name: JHOC5 cells infected with SPINK1 knockdown virus #9 replicate c


title: immvarYE_8-30_4

description: sle.mtx


title: YE_7-13-3

description: sle.mtx


title: JHOC5 IL-6 KD#58 replicate a

description: Gene expression data from cell culture

source_name: JHOC5 cells infected with IL-6 knockdown virus #58 replicate a


title: immvarYE_0907_3

description: sle.mtx

source_name: Peripheral blood mononuclear cells


title: immvarYE_0907_4

description: sle.mtx


title: immvarYE_0907_2

description: sle.mtx


title: JHOC5 NT (control) Experiment A replicate a

description: Gene expression data from cell culture

source_name: JHOC5 cells infected with NT control lentivirus experiment A replicate a


title: JHOC5 SPINK1 KD #9 replicate e

description: Gene expression data from cell culture

source_name: JHOC5 cells infected with SPINK1 knockdown virus #9 replicate e


title: immvarYE_0907_1

description: sle.mtx


title: immvarYE_0831_4

description: sle.mtx


title: JHOC5 NT (control) Experiment C replicate c

description: Gene expression data from cell culture

source_name: JHOC5 cells infected with NT control lentivirus experiment C replicate c


title: shASCL1#3_dup2

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

description: processed data file: DEG_ASCL1_KD.txt

data_processing:
RNA-seq datasets of two control samples and two knockdown samples were aligned to the hg19 human genome using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1.
htseq-count v0.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation.
Bioconductor package DESeq2 v1.12.4, with the intersection-strict mode, was used to analyze differential gene expression.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *txt: htseq-count files.
Supplementary_files_format_and_content: DEG_ASCL1_KD.txt: Tab-delimited text file for differentially expressed genes.

source_name: Kelly cells

growth_protocol: Kelly cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.

extract_protocol:
Total RNA was harvested using the miRNeasy Mini Kit (Qiagen).
Non-strand-specific library construction and sequencing of paired-end, 100-bp-long reads by the BIGSeq-500 were performed at the BGI Biotech Solutions.

treatment_protocol: Kelly cells were infected with the shRNA-expressing lentivirus. Puromycin selection was carried out 36 hours post infection, after which total RNA were harvested.

value: Kelly

value: Neuroblastoma

tag: knockdown


title: immvarYE_0831_3

description: sle.mtx


title: shGFP_dup2

description: processed data file: DEG_ASCL1_KD.txt

value: Control


title: immvarYE_0831_2

description: sle.mtx


title: JHOC9 IL-6 KD#58 replicate d

description: Gene expression data from cell culture

source_name: JHOC9 cells infected with IL-6 knockdown virus #58 replicate d


title: immvarYE_0831_1

description: sle.mtx


title: shGFP_dup1

description: processed data file: DEG_ASCL1_KD.txt


title: HB5b-48hpi

city: Athens

first: Mark

middle: Daniel

last: Slayton

state: Ohio

address: 7 Depot Street

department: Biomedical Sciences

institute: Ohio University

description:
HB5-48hpi_sample B
processed data file: 888 versus hb5 48 hpi.xlsx

data_processing:
Illumina CASAVA 1.8 was used for basecalling.
Reads were trimmed and aligned to a composite genome containing the human and human cytomegalovirus genomes in CLC Genomics Workbench, Version 9.0.
TPM (Transcripts per Kilobase Million) was determined for each sample with the CLC Genomics Workbench RNA-seq analysis module via EDGE analysis.
Transcripts with less than 20 unique reads were discarded as background.
Genome_build: GRCh39.p10 (Homo sapeins), FJ527563.1 (Human cytomegalovirus)
Supplementary_files_format_and_content: XML spreadsheet containing transcript abundance measurements for each sample

organism:
Homo sapiens
Human betaherpesvirus 5

source_name: HCMV WT infected human fibroblasts_48hpi

extract_protocol:
RNA was extracted from infected cells at the indicated times post infection with Direct-zol RNA purification columns or Qiagen RNA easy kits per the manufacturer's instructions.
Strand-specific RNA library construction and sequencing were performed on duplicate biological samples for each virus and time point by Admera Health, South Plainfield, NJ and the team at Admera Health LLC

value: human fibroblasts

tag: infected with

value: HCMV wild-type

tag: hours post-infection

tag: moi of infection

value: 1 pfu/cell


title: shASCL1#3_dup1

description: processed data file: DEG_ASCL1_KD.txt


title: JHOC9 IL-6 KD#58 replicate b

description: Gene expression data from cell culture

source_name: JHOC9 cells infected with IL-6 knockdown virus #58 replicate b

tag: tissue


title: shMYCN#1_dup2

data_processing:
RNA-seq datasets of two control samples and two knockdown samples for LMO1 and MYCN were aligned to the hg19 human genome using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1.
htseq-count v0.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation
Bioconductor package DESeq2 v1.12.4, with the intersection-strict mode, was used to analyze differential gene expression.
Genome_build: hg19
Supplementary_files_format_and_content: txt file for differentially expressed genes
Supplementary_files_format_and_content: htseq-count file

extract_protocol:
Total RNA was harvested using the miRNeasy Mini Kit (Qiagen).
Reverse-stranded library construction and sequencing of paired-end, 100-bp-long reads by the BGISeq500 were performed at the BGI Biotech Solutions

tag: shRNA

value: MYCN knockdown


title: flare4-4

description: flare.mtx

value: SLE flare


title: 888b-48hpi

description:
889 48 hpi_sample B
processed data file: 888 versus hb5 48 hpi.xlsx

source_name: HCMV UL34COOH mutant infected human fibroblasts_48hpi

value: HCMV UL34COOH mutant


title: shMYCN#1_dup1


title: SHSY-5Y_shLMO1#2_dup2

hyb_protocol: Standard Affymetrix 3' array hybridyzation protocol.

scan_protocol: Standard Affymetrix confocal laser scanner protocol.

data_processing: Array signals were normalized using RMA (http://rmaexpress.bmbolstad.com/).  Differential gene expression was determined using a moderated t-test in the “limma” package (http://bioinf.wehi.edu.au/limma/) from Bioconductor (www.bioconductor.org).

label_protocol: Standard Affymetrix biotin label protocol.

growth_protocol: SHSY-5Y cells was cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.

extract_protocol: After 72 hours of infection, total RNA was harvested by Qiazol followed by a column purification using RNeasy Mini kit (Qiagen) following manufacturer's instruction.

treatment_protocol: SHSY-5Y cells was infected with lentivirus encoding shRNA. The infected cells were selected by puromycin.

value: Neuroblastoma cell line

tag: genotype/variation

value: LMO1 (shLMO1#2)


title: JHOC9 SPINK1 KD #9 replicate b

description: Gene expression data from cell culture

source_name: JHOC9 cells infected with SPINK1 knockdown virus #9 replicate b


title: JHOC9 SPINK1 KD #9 replicate c

description: Gene expression data from cell culture

source_name: JHOC9 cells infected with SPINK1 knockdown virus #9 replicate c


title: flare4-3

description: flare.mtx


title: 888a-48hpi

description:
888 48 hpi_sample A
processed data file: 888 versus hb5 48 hpi.xlsx


title: SHSY-5Y_shGFP_dup1

value: control GFP shRNA (shGFP)


title: flare4-2

description: flare.mtx


title: shLMO1#2_dup2

value: LMO1 knockdown


title: JHOC5 NT (control) Experiment B replicate b

description: Gene expression data from cell culture

source_name: JHOC5 cells infected with NT control lentivirus experiment B replicate b

value: Ovarian clear cell carcinoma


title: SHSY-5Y_shLMO1#2_dup1


title: HB5b-4hpi

description:
HB5-4hpi_sample B
processed data file: 888 versus hb5 4 hpi.xlsx

source_name: HCMV WT infected human fibroblasts_4hpi


title: JHOC9 NT (control) Experiment D replicate d

description: Gene expression data from cell culture

source_name: JHOC9 cells infected with NT control lentivirus experiment D replicate d


title: HB5a-48hpi

description:
HB5-48hpi_sample A
processed data file: 888 versus hb5 48 hpi.xlsx


title: shLMO1#2_dup1


title: flare4-1

description: flare.mtx

value: PBMCs


title: JHOC9 NT (control) Experiment E replicate e

description: Gene expression data from cell culture

source_name: JHOC9 cells infected with NT control lentivirus experiment E replicate e


title: HB5a-4hpi

description:
HB5-4hpi_sample A
processed data file: 888 versus hb5 4 hpi.xlsx


title: JHOC9 NT (control) Experiment C replicate c

description: Gene expression data from cell culture

source_name: JHOC9 cells infected with NT control lentivirus experiment C replicate c


title: JHOC9 SPINK1 KD #9 replicate a

description: Gene expression data from cell culture

source_name: JHOC9 cells infected with SPINK1 knockdown virus #9 replicate a


title: Lung E18.5 Bim3'UTRmut/mut 9

city: Innsbruck

first: Verena

last: Labi

address: Innrain 80-82

department: Developmental Immunology

country: Austria

institute: Medical University Innsbruck

description:
miRNA
SAMPLE 9

hyb_protocol: NanoString Technologies GXA-MMIR15-12; See manufacturer instructions at https://www.nanostring.com/products/mirna-assays/mirna-panels

data_processing: none - raw data were used for analysis

source_name: E18.5 murine total lung tissue

label_protocol: Continuous sample labeling

extract_protocol: Total RNA was extracted from E18.5 lung tissue ground into powder in liquid nitrogen with a mortar and pestle using the miRNeasy mini kit (QIAGEN 217004). The concentration and purity of RNA was assessed using a NanoDrop spectrophotometer (Thermo Scientific). Samples with A260/280 ratios <2.0 and A260/230 ratios <1.5 were excluded from analysis. 100 ng of total RNA per sample was used as input for nCounter gene expression analysis (NanoString Technologies).

tag: developmental stage

value: embryo

tag: age

tag: strain (genetic background)

tag: genotype

value: lung


title: SHSY-5Y_shGFP_dup2


title: JHOC9 NT (control) Experiment A replicate a

description: Gene expression data from cell culture

source_name: JHOC9 cells infected with NT control lentivirus experiment A replicate a


title: shGFP_dup2

extract_protocol:
Total RNA was harvested using the miRNeasy Mini Kit (Qiagen).
Reverse stranded library construction and sequencing of paired-end, 100-bp-long reads by the BGISeq500 were performed at the BGI Biotech Solutions

value: control


title: JHOC9 NT (control) Experiment B replicate b

description: Gene expression data from cell culture

source_name: JHOC9 cells infected with NT control lentivirus experiment B replicate b


title: 888b-4hpi

description:
889 4 hpi_sample B
processed data file: 888 versus hb5 4 hpi.xlsx

source_name: HCMV UL34COOH mutant infected human fibroblasts_4hpi


title: shGFP_dup1

source_name: Kelly cells

value: Neuroblastoma


title: flare3-3

description: flare.mtx

source_name: Peripheral blood mononuclear cells

tag: condition

value: primary cells


title: Lung E18.5 Bim3'UTRmut/mut 8

description:
miRNA
SAMPLE 8

scan_protocol: NanoString Technologies GXA-MMIR15-12; See manufacturer instructions at https://www.nanostring.com/products/mirna-assays/mirna-panels


title: 888a-4hpi

description:
888 4 hpi_sample A
processed data file: 888 versus hb5 4 hpi.xlsx

value: human fibroblasts


title: Lung E18.5 Bim3'UTRmut/mut 7

description:
miRNA
SAMPLE 7


title: Lung E18.5 Bim3'UTRmut/mut 6

description:
miRNA
SAMPLE 6


title: WT+SA187 replicate 3

city: Thuwal

first: Hanin

last: ALZUBAIDY

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

description: after 5 days of germination and SA187 inoculation seedlings were transferred to plates with 100mM NaCl for 16 days

data_processing:
RNA-seq was carried out on three independent biological replicates. Library preparation and sequencing was performed on HiSeq 4000 platform using Illumina 1.9 encoding resulting in 150 bps paired-end reads. About 50 million reads per sample was generated. Sequenced reads were checked for quality using FASTQC v0.11.5
Adapters and low-quality reads or bps were filtered using Trimmomatic 0.36 (Bolger, Lohse, & Usadel, 2014), retaining first 100 bps and by using the default settings available for paired-end reads in Trimmomatic. The trimmed reads were then cross-checked for quality and were aligned to the Arabidopsis thaliana reference genome (TAIR10) using Tophat v2.1.1with 2bp mismatches reporting one maximum hit. The annotation file was provided as reference for reads alignment. MultibamSummary from deepTools2 package
Summary of read counts per gene was calculated using featureCounts v1.5.1 (Liao, Smyth, & Shi, 2014). FPKM for individual replicates was calculated using Cufflinks v.2.2.1 (Trapnell et al., 2012). Differentially expressed genes between two conditions were identified using CuffDiff tool from Cufflinks package v2.2.1 (Trapnell et al., 2012) using quartile normalization. Genes with 2-fold change and P value <= 0.05 were considered as significantly different between samples with and without hrcc treatment, with and without SA187 treatment, under normal conditions against salt stress conditions.
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKM in txt

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: root

extract_protocol:
roots were cut, flash frozen in liquid nitrogen, and RNA was harvested using the Nucleospin RNA plant kit (Macherey-Nagel). Illumina Truseq_HT_hiseq4000 RNA Sample Prep Kit  was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ecotype

value: 21 days

value: root


title: flare3-4

description: flare.mtx

tag: sample type

tag: chip antibody


title: WT+SA187  replicate 2


title: WT+SA187  replicate 1


title: flare2-2

description: flare.mtx

tag: cell type


title: Lung E18.5 wild type 5

description:
miRNA
SAMPLE 5

value: wild type


title: flare2-1

description: flare.mtx

value: SLE flare


title: WT replicate 2

description: after 5 days of germination seedlings were transferred to plates with 100mM NaCl for 16 days


title: flare3-1

description: flare.mtx


title: flare3-2

description: flare.mtx


title: WT replicate 3


title: Lung E18.5 wild type 4

description:
miRNA
SAMPLE 4


title: Lung E18.5 wild type 3

description:
miRNA
SAMPLE 3


title: CNV 3

city: Changsha

first: Yedi

state: Hunan

address: No. 139, Middle Renmin Road

department: Department of Ophthalmology

institute: The Second Xiangya Hospital, Central South University

description: circRNA expression data from sampes of laser-induced CNV mice

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Mouse circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 3 out of 6 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information.

source_name: RPE-choroid-sclera complexes from laser-induced CNV eye (7 days after the laser photocoagulation)

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

growth_protocol: The animals were maintained in cages in temperature-controlled rooms featuring a 12-h light/12-h dark cycle.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The photocoagulation was applied in eyes of mice around the optic disc using a 532-nm diode laser (100 mW, 0.1 s duration, 50 μm).  Twenty-five spots were burned on each eye, and the eyes were enucleated at 7 days after the laser photocoagulation. Age-matched mice without laser photocoagulation treatment were used as controls.

value: RPE-choroid-sclera complexes

tag: disease state

value: laser-induced CNV

tag: gender

value: male


title: flare1-1

description: flare.mtx


title: WT replicate 1


title: Lung E18.5 wild type 2

description:
miRNA
SAMPLE 2


title: Lung E18.5 wild type 1

description:
miRNA
SAMPLE 1


title: flare1-2

description: flare.mtx